Refactor: address KISS and DRY violations (#70)

[GiggleLiu]

Summary

• DRY Roadmap #1: Trim duplicated delegation methods from 5 graph problem structs (~325 lines removed) — callers use problem.graph().method() directly
• DRY Implement remaining reduction rules #2: Implement BipartiteGraph and PlanarGraph as validated SimpleGraph wrappers with proper VariantParam registration
• KISS feat: Feature parity with ProblemReductions.jl #4: Extract classify_problem_category, filter_redundant_base_nodes, and is_natural_edge helpers from the 190-line to_json() monolith
• Docs: Polish design.md with variant system section, lattice diagrams, and improved trait hierarchy visuals
• Style: Apply rustfmt formatting across touched files

Closes #70

Test plan

• All 1487 unit tests pass
• All 47 doc tests pass
• Clippy clean (zero warnings)
• CI passes

🤖 Generated with Claude Code

[codecov]

Codecov Report

❌ Patch coverage is 97.00000% with 15 lines in your changes missing coverage. Please review.
✅ Project coverage is 96.77%. Comparing base (a4264a6) to head (9135218).
⚠️ Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
src/topology/planar_graph.rs	72.41%	8 Missing ⚠️
src/topology/kings_subgraph.rs	0.00%	3 Missing ⚠️
src/rules/graph.rs	93.54%	2 Missing ⚠️
src/topology/bipartite_graph.rs	96.77%	2 Missing ⚠️

Additional details and impacted files

@@           Coverage Diff            @@
##             main      #71    +/-   ##
========================================
  Coverage   96.76%   96.77%            
========================================
  Files         185      189     +4     
  Lines       25789    25906   +117     
========================================
+ Hits        24955    25070   +115     
- Misses        834      836     +2     

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[Copilot]

Pull request overview

Refactors the variant-aware reduction graph and several graph problem models to remove duplicated delegation APIs (KISS/DRY), while introducing validated topology wrappers (PlanarGraph, BipartiteGraph) and improving reduction-graph JSON generation + docs/diagrams.

Changes:

• Remove duplicated graph/weight delegation methods from multiple graph problems; update call sites to use problem.graph().* and problem.weights().
• Add PlanarGraph and BipartiteGraph as SimpleGraph-backed topology types with validation and VariantParam registration.
• Extract filter_redundant_base_nodes, classify_problem_category, and is_natural_edge helpers; update docs/diagrams and formatting.

Reviewed changes

Copilot reviewed 71 out of 78 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
tests/suites/reductions.rs	Update tests to use graph() accessors
tests/suites/integration.rs	Switch weighted tests to with_weights
src/unit_tests/unitdiskmapping_algorithms/weighted.rs	Rustfmt-only cleanup in tests
src/unit_tests/unitdiskmapping_algorithms/mapping_result.rs	Import ordering cleanup in tests
src/unit_tests/unitdiskmapping_algorithms/julia_comparison.rs	Formatting cleanup in assertions
src/unit_tests/unitdiskmapping_algorithms/gadgets_ground_truth.rs	Rustfmt cleanup for macros
src/unit_tests/topology/planar_graph.rs	Add unit tests for PlanarGraph
src/unit_tests/topology/bipartite_graph.rs	Add unit tests for BipartiteGraph
src/unit_tests/rules/unitdiskmapping/triangular/mod.rs	Formatting cleanup in tests
src/unit_tests/rules/unitdiskmapping/triangular/mapping.rs	Formatting cleanup in tests
src/unit_tests/rules/sat_minimumdominatingset.rs	Update tests to use graph()
src/unit_tests/rules/sat_maximumindependentset.rs	Update tests to use graph()
src/unit_tests/rules/minimumvertexcover_maximumindependentset.rs	Update weights/graph assertions
src/unit_tests/rules/maximumindependentset_triangular.rs	Update tests to use graph()
src/unit_tests/rules/maximumindependentset_maximumsetpacking.rs	Update tests to use graph()
src/unit_tests/rules/maximumindependentset_gridgraph.rs	Update tests to use graph()
src/unit_tests/rules/maximumclique_ilp.rs	Update tests to use graph()/weights slice
src/unit_tests/rules/graph.rs	Add helper-focused tests for graph JSON export
src/unit_tests/models/satisfiability/ksat.rs	Add KN-focused tests
src/unit_tests/models/graph/minimum_vertex_cover.rs	Update tests to use graph()/weights slice
src/unit_tests/models/graph/minimum_dominating_set.rs	Update tests to use graph()/weights slice
src/unit_tests/models/graph/maximum_independent_set.rs	Update tests to use graph()/weights slice
src/unit_tests/models/graph/maximum_clique.rs	Update tests to use graph()/weights slice
src/unit_tests/models/graph/maximal_is.rs	Update tests to use graph()/weights slice
src/unit_tests/io.rs	Update IO tests to use graph()
src/unit_tests/graph_types.rs	Adjust tests for new topology types
src/unit_tests/graph_models.rs	Update tests to use graph()/weights slice
src/topology/planar_graph.rs	Introduce validated PlanarGraph wrapper
src/topology/mod.rs	Wire in new topology modules/exports
src/topology/kings_subgraph.rs	Formatting-only change
src/topology/bipartite_graph.rs	Introduce BipartiteGraph topology type
src/rules/unitdiskmapping/weighted.rs	Formatting-only change
src/rules/sat_ksat.rs	Formatting-only change
src/rules/minimumvertexcover_qubo.rs	Use graph() + weights slice
src/rules/minimumvertexcover_minimumsetcovering.rs	Use graph() + weights slice
src/rules/minimumvertexcover_maximumindependentset.rs	Use graph() + weights slice
src/rules/minimumvertexcover_ilp.rs	Use graph() + weights slice
src/rules/minimumdominatingset_ilp.rs	Use graph() accessor
src/rules/maximumindependentset_triangular.rs	Use graph() accessor
src/rules/maximumindependentset_qubo.rs	Use graph() + weights slice
src/rules/maximumindependentset_maximumsetpacking.rs	Use graph() + weights slice
src/rules/maximumindependentset_ilp.rs	Use graph() accessor
src/rules/maximumindependentset_gridgraph.rs	Use graph() accessor
src/rules/maximumclique_ilp.rs	Use graph() accessor
src/rules/graph.rs	Extract helpers used by to_json()
src/models/satisfiability/ksat.rs	Allow KN without clause-length validation
src/models/graph/minimum_vertex_cover.rs	Remove delegation APIs; expose weights slice
src/models/graph/minimum_dominating_set.rs	Remove delegation APIs; expose weights slice
src/models/graph/maximum_independent_set.rs	Remove delegation APIs; expose weights slice
src/models/graph/maximum_clique.rs	Remove delegation APIs; expose weights slice
src/models/graph/maximal_is.rs	Remove delegation APIs; expose weights slice
src/graph_types.rs	Remove Planar/Bipartite marker types
examples/reduction_satisfiability_to_minimumdominatingset.rs	Update example to use graph()
examples/reduction_satisfiability_to_maximumindependentset.rs	Update example to use graph()
examples/reduction_minimumvertexcover_to_qubo.rs	Update example to use graph()
examples/reduction_minimumvertexcover_to_minimumsetcovering.rs	Update example to use graph()
examples/reduction_minimumvertexcover_to_maximumindependentset.rs	Update example to use graph()
examples/reduction_minimumvertexcover_to_ilp.rs	Update example to use graph()
examples/reduction_minimumdominatingset_to_ilp.rs	Update example to use graph()
examples/reduction_maximumindependentset_to_qubo.rs	Update example to use graph()
examples/reduction_maximumindependentset_to_minimumvertexcover.rs	Update example to use graph()
examples/reduction_maximumindependentset_to_maximumsetpacking.rs	Update example to use graph()
examples/reduction_maximumindependentset_to_ilp.rs	Update example to use graph()
examples/reduction_maximumclique_to_ilp.rs	Update example to use graph()
examples/export_petersen_mapping.rs	Formatting-only change
examples/export_mapping_stages.rs	Formatting-only change
docs/src/static/variant-hierarchy.typ	Diagram layout tweak
docs/src/static/variant-hierarchy.svg	Regenerated diagram asset
docs/src/static/trait-hierarchy.typ	Update trait hierarchy diagram
docs/src/static/lattices.typ	New lattice/topology diagram source
docs/src/getting-started.md	Expand reduction chaining explanation
docs/src/design.md	Major variant/reduction graph doc refresh
Makefile	Adjust Typst diagram compilation

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[Copilot]

test_classify_problem_category uses a module path containing models::sat::..., but the crate's models module is models::satisfiability (see existing test_category_from_module_path expectations). This makes the test (and/or the helper contract) inconsistent and likely failing. Update the test input to use problemreductions::models::satisfiability::... (or adjust classify_problem_category to intentionally map satisfiability -> sat, but then align the other tests and call sites).